Low Stomach Acid and Autoimmune Disease

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One of the recent topics I have covered in my coursework with the Nutritional Therapy Association is digestion. In the book Why Stomach Acid Is Good For You by Dr. Jonathan Wright, I have come across a lot of information that I believe is relevant to those suffering with autoimmune disease and dealing with digestive difficulties (considering leaky gut — probably all of us!). Here I will answer some key questions on the topic of stomach acid.

Why is stomach acid important?

Stomach acid is responsible for optimizing gastric pH and triggering the action of pepsin, an enzyme that is needed to break protein down into amino acids and peptides. If the pH of the stomach is not optimal, then nutrients are not broken down into absorbable components and protein digestion is compromised. Stomach acid also prevents bacterial and fungal overgrowth. When it is properly acidic, bacteria that are ingested along with food don’t stand a chance. It acts as an acid buffer to protect the body from pathogens that enter our bodies.

I thought too much stomach acid was the problem — how can it be a problem of too little?

Unfortunately, instead of being actually checked for stomach acid levels, anyone who goes to the doctor complaining of heartburn or GERD gets sent home with a prescription for an acid-blocking or proton-pump inhibiting drug. What is incredible is that the symptoms of having too little stomach acid can be the same as having too much – which medically is rare. When actually tested for stomach acid levels, most people with these problems actually have low stomach acid. The job of the pyloric sphincter (valve that lets food from the stomach into the small intestine) is to make sure the food is properly acidified before it passes on to the next phase of digestion. When a person has low stomach acid, that valve doesn’t want to led the food pass because it is not at the proper pH. This causes food to sit and putrefy in the stomach, and eventually pushes up on the lower esophageal sphincter causing symptoms of reflux and heartburn.

What kind of problems can low stomach acid contribute to?

Low stomach acid, or hypochlorhydria, can be responsible for a myriad of problems. First, low acid levels mean lower absorption of nutrients such as amino acids, iron, calcium, folic acid, vitamin b12, zinc, and others. The impact of this can be great – a person could be eating the most nutritionally complete diet, but if they don’t have sufficient stomach acid, a lot of these nutrients can go to waste and not end up being properly assimilated into the body. It can also make us more vulnerable to bacterial infections, parasites, and fungal overgrowth. Low stomach acid is associated with allergies, depression, anemia, stomach cancer, skin problems, gallbladder disease, osteoporosis, autoimmune disease, and accelerated aging.

How does stomach acid relate to autoimmune disease?

According to Dr. Wright’s research, people with autoimmune disease tend to have low stomach acid, poor digestion, and multiple food allergies. In his book, he talks about how he is surprised when he has a patient with autoimmune disease that does not have low stomach acid! Allergic reactions cause the gastric and intestinal linings to become inflamed, decreasing the secretion of stomach acid and causing allergic reaction symptoms elsewhere on the body (as on the skin). Prolonged exposure to allergens or irritants contributes to leaky gut, or intestinal permeability, which is already a well-researched feature of autoimmune disease. These proteins that are able to pass through the intestinal barrier can cause a person’s autoimmune symptoms to worsen. It is very important that those with autoimmune disease maintain the correct gastric pH so that their proteins get properly broken down and don’t end up in the blood stream. The byproducts of bacterial overgrowth in the small intestine (SIBO) can harm the intestinal lining even further, promoting a leaky gut even when allergens have been removed from the diet.

How do I know if I have low stomach acid?

Chances are, if you have had problems with heartburn or indigestion in the past (especially if you have taken proton pump inhibitors for long periods of time) you could have low stomach acid. The risk is higher for those who have malabsorption, vitamin and mineral deficiencies, digestive problems, autoimmune disease, or have been vegan or vegetarian. It is important to work with a provider to determine if you have low stomach acid before trying supplementation with HCL.

How can I increase my production of stomach acid?

Once you have carefully determined that you have low stomach acid with the help of a practitioner, you have a few ways to help your body make more or supplement. Bitters are natural herbs that stimulate the stomach to make more acid. They need to be taken in small doses and tasted in order to have the medicinal bitter effect. Some of the herbs include caraway, dandelion, fennel, ginger, goldenseal, milk thistle, peppermint, and yellow dock. If that doesn’t work, taking a couple of tablespoons of apple cider vinegar or lemon juice at the beginning of a meal can help acidify the contents of the stomach. If you are quite low on stomach acid, supplementary HCL tablets may be beneficial. If you are planning on supplementing with HCL, I highly recommend working with a medical practitioner to ensure that it is safe for you to do so.

My personal experience with low stomach acid:

When I was deep in my illness I was struggling desperately with multiple vitamin and mineral deficiencies. I was very low on iron, b12, and vitamin d, among other things. I had been vegan for a long time, and my digestion was very weak. No manner of supplementation was helping any of my deficiencies. My practitioner had me do a HCL test, and we found that I had one of the worst cases of low stomach acid that she had ever seen in her practice. She put me on supplemental HCL, and I felt that my digestion was improving. Then I started eating meat, and I suddenly needed half the amount of pills I had been taking. This made sense because zinc and b1 are required for stomach acid production, and both nutrients can easily be deficient in a vegan diet. I got a blood test and my vitamin and mineral status was back to normal, for the first time in years. I believe that my autoimmune diseases as well as being vegan for so long contributed to my low stomach acid. I still take HCL supplements, but nowhere near the quantities that I did before. I believe that getting my stomach acid on track has been a huge part of ensuring that the nourishing diet that I eat gets all the way to my cells.

Mickey Trescott is a cook and one of the bloggers behind Autoimmune Wellness. After recovering from her own struggle with both Celiac and Hashimoto’s disease, adrenal fatigue, and multiple vitamin deficiencies, Mickey started to write about her experience to share with others and help them realize they are not alone in their struggles. She is a certified Nutritional Therapy Practitioner by the Nutritional Therapy Association, and is the author of The Autoimmune Paleo Cookbook, a guide and recipe book for the autoimmune protocol, and AIP Batch Cook, a video-based batch cooking program. You also can find her on Instagram.

48 comments

Hi, The link that I provided above at SCD lifestyle goes over some testing options, one your doctor can do and two you can do at home. I have always used the home test as the one at the doctors is quite expensive.

Reblogged this on primally kosher and commented: I started taking one to two betaine HCL’s after eating a meal. I wanted to see if my digestion will improve. I have a feeling it takes close to a month to really see a difference. 2 pills make my stomach gurgle. 1 seems to eliminate some of the heaviness I get after I eat.

Thanks for updating me on your progress! Gurgling could be a sign of taking too much, but you will know if that is what it is. If you are lacking in HCL, you will notice the feeling that food moves out of your stomach instead of taking a long time to digest.

I noticed a difference in my digestion right away once I got on the right dose, but it was slow working up (my practitioner was very cautious). After that it was another couple of months before my deficiencies went away – I also started eating meat during that time. It has been over a year and I still take HCL, although nowhere near as much as I used to. I can really tell when I don’t take it and make sure to have some with every meal 🙂

[…] I wonder how long it will take before I notice other positive effects. Low stomach acid can cause a myriad of other issues (including fungal overgrowths!). If I'm not processing proteins properly, it makes sense that I […]

I am so glad I found your site. It is amazing and I’m learning a lot. One suggestion – when you link to someone else’s page, click the box that says open page in a new window. That way people don’t get lost, I always have your page to return to. Got the book and I will work my way through all the information. Thanks so much, Pam

I have been on PPI’s for years. I have tried to stop them, but my heartburn is so severe I have not been able to get off of them. They are made so you have to take them for life (someone in big Pharma admitted to it) and my Dr. Told me the same. How do I get off of them? I am very deficient in all nutrients and have severe digestive problems. I have been on your AIP protocol for almost two months. Any thoughts? Thanks!

I have the same problem I have to take them 2x a day, maybe since I’m eating more cultured and fermented foods and drinks that I make at home I will try to cut back to once a day and see what happens, and will get real ACV, and take it from there, unfortunately I’m on Medicaid and they don’t pay for holistic health care, but they gladly pay for all the medications that end up causing more harm than good.

Mickey, I have severe reflux and an endoscopy revealed a hiatus hernia. It also revealed that my stomach was full of breakfast that I’d eaten 7 hrs previously. I have been thinking about HCL but I’m concerned that the hernia will allow too much acid through. Any advice? Many thanks, C

It,s called gastroenteritis, it’s when your food digests to slowly, I have had that problem myself, After I did a gentle cleanse, used essential oils topically, just ones from the health food store, you don’t have to get Young’s or DoTerra, the things they suggest are not safe,and then added cultured and ferments to my dirty,and included some yoga for digestion, and went gluten free, I still have problems occasionally, but I think it’s mostly when I accidentally eat gluten or don’t get enough ferments in me

Hi Mickey, I have a question: I was diagnosed with GERD many years ago and told to take PPIs – terrible advice that I’ve steadfastly ignored. I also have Hashimoto’s and have (so far) been able to manage my condition reasonably well through diet alone. I have been gluten-, soy-, corn-, nightshade, and dairy-free for almost three years, and AIP-friendly for a month or so. I am convinced of a gut-thyroid connection, and feel confident that my road to healing starts in my gut. But I’m confused…my only overt, digestion-related symptom is what I would call ‘burning stomach’ (NO heartburn, but a narrowing of the esophagus that the (horrible) gastroenterologist (who prescribed PPIs) says is due to acid reflux / scar tissue). I have been operating under the assumption that I have low stomach acid, but when I try things like taking raw apple cider vinegar (or lemon juice) in an ounce or so of water to dilute, the burning pain in my stomach is almost instantly severe…leading me to question whether high stomach acid could be the culprit. (I am also a single mother and full-time PhD student, so I know stress plays a role in this as well.) Given my reactivity to apple cider vinegar, I’m scared to try HCI! I might add, by the way, that I have apple cider vinegar in my olive-oil-based salad dressing every night without issue – it’s just drinking it straight that produces pain! Introducing ground beef on the AIP has also increased the burning sensation, which is why I’ve been assuming that I have low stomach acid, causing food (like ground beef) to “sit and putrefy in the stomach”, as you’ve described above. Any thoughts? I’m so confused. Thank you!!

Lyra, It does sound more likely that your issue could be chronic low stomach acid, especially considering your reaction to meat. That being said, I would not experiment with HCL without the supervision of a practitioner in this case. You could need the acid, but you may need to go through a protocol to heal the stomach lining before you can tolerate more acid. I would suggest looking for a functional medicine practitioner to help on this one. Good luck!

Thank you, Mickey. It’s a little overwhelming sometimes, trying to piece all of the information together. What you’ve said makes a lot of sense (I can almost feel my stomach lining breathing a sigh of relief). Now – fingers crossed I can actually find a good functional medical practitioner! Thank you, also, for everything you do (sharing your story, blog, cookbook…). I can’t tell you how much it has meant to me, personally, to know that there is someone else out there with Hashimotos who is finding healing through food. And your willingness to share your experiences (e.g. with HCL, AIP, Whole30…) means that people like me are better-equipped to navigate the bumps in the road, and feel much less isolated along the way. Keep up the great work. I wish you continued success on your journey.

I recently moved to North Carolina and am finding my way through new doctors. My family doctor recommended I see a gastroenterologist due to results of a stool test. The test showed low pancreatic enzymes, no measurable amount of lactobacillus, and a low amount of bifidobacteria.

The visit with the GI doc was so frustrating! He doesn’t think the stool test is valid because it lacks scientific evidence, so he says he has no idea what to do with the results. He thinks the HCL supplements I take are causing my symptoms, when in fact, taking them eliminates my indigestion, gas, and bloating! He wants me to stop taking them, start taking a prescription acid-reducer, and have an endoscopy and colonoscopy in three to four weeks. (I had those tests 1 1/2 years ago, so it seems odd to do them again so soon.)

I have been quite stressed by the fact that he disagrees with practically everything I believe, though I certainly don’t have all my answers yet. I have decided to continue with the AIP, which I started easing into on Feb. 25th, and continue trusting my body. I just cannot fathom stopping these HCL supplements, which are clearly helping me digest my food. I might do the tests if I don’t see the improvement I seek, but frankly, I believe I would first schedule a consultation with you!

I have Hashimoto’s and possibly celiac disease. (I gave up gluten in 2006 before I or my doctors knew to test me for celiac disease. However, I have two copies of the HLA DQ2 gene, so I am at high risk for developing it, if I haven’t already.)

Hi Alysson, I know how frustrating it can be to work with doctors who do not sympathize with your efforts, and give the opposite advice. While I can’t tell you to disobey your doctors orders, you do know that nobody can force you to do anything with your body. It sounds like you are doing a good job of listening to your intuition and getting at the root of your issues. I’d be happy to help you, but just know that I can’t advise you to do anything that is against the orders of your doctor, since I am not one. I do a lot of coaching with Hashimoto’s patients, helping them formulate questions for their doctors as well as going through the elimination diet.

Thanks for your reply and for wishing me luck! Thanks, too, for the reminder about your role as an AIP coach. I understand that you need to limit your recommendations to the scope of your training.

I have decided to continue taking the HCL supplements and not start the prescription acid-reducer. In fact, I recently went to an applied kinesiologist to have all my supplements and prescription medications tested. My body said yes to the HCL but no to the acid-reducer. My body said no to a number of other supplements I was taking, so I have stopped them as well.

I also decided to wait until the end of August for the colonoscopy and endoscopy to give the AIP more time. (The gastroenterologist did say he would be willing to work with me even if I don’t follow all or any of his recommendations. I do appreciate that about him.)

The applied kinesiologist also found infections (bacterial, viral, and parasitic), so I will see what the next step is there.

I will be in touch soon about scheduling a session with you if I don’t see more progress within the next month. (If I weren’t in a negative cash flow situation right now, I would contact you today!)

I actually see a functional medicine practitioner who uses applied kinesiology to help me suss out my supplement regimen and have found it very helpful (with the addition of using my NTP training, and running everything by my doc to make sure).

I also recommend Metametrix testing (They have a test called the GI Effects Panel that you can order yourself on mymedlab.com) to diagnose any gut infections suspected by the kinesiologist before undergoing any antimicrobial regimen. This is also something your GI doc could possibly order (unfortunately insurance doesn’t usually cover it). I talk about my experience with this test here:

I am on AIP since May 1. Since I have leaky gut and nutritional deficiencies, I’m sure I have low stomach acid….so I tried the Betaine test and took one pill before each meal for two weeks when I had to stop as indigestion and bloating were so bad….doctor said take Digestzyme…..did that…indigestion did not go away….it continued for another week and then quit. The indigestion went away…..don’t know what to do….could it be that I don’t have low stomach acid? I doubt it. doctor said he doesn’t have a clue….maybe it was too strong? proper acid is important to my healing…don’t know what to do.

Hi Ruth, unfortunately I am not a medical practitioner and can’t help you troubleshoot this issue. If your practitioner does not know how to work with low stomach acid I would find a different one who can properly diagnose and treat you. Good luck!

[…] it’s no surprise that we think we have too much stomach acid. Actually, the opposite is true. Mickey wrote a great article explaining how this works, but the quick summary is this: We need stomach acid to digest our food, […]

Thanks for a great article on an important topic! One clarification regarding bitters: “Some of the herbs include caraway, dandelion, fennel, ginger, goldenseal, milk thistle, peppermint, and yellow dock.” Caraway, fennel and peppermint are not bitters, they are usually included in bitters formulas for their carminative action (decreasing gas). Milk thistle is a liver tonic, but not really a bitter. Urban Moonshine and Herb Pharm are two companies who make great bitters. Guido Mase is a great source of information about bitters.

Hi James – I believe both are true, but with autoimmune disease it isn’t as simple. I think of it more like autoimmune disease can cause conditions that lead to low stomach acid, and low stomach acid leads to deficiencies that lead to or worsen autoimmune disease.

Hi Mickey, thanks for the informative article. I believe that low stomach acid may be responsible for my symptoms, as I have issues with digestion on a healthy plant-based diet, have abdominal discomfort and bloating, have struggles with cystic acne, low energy levels amongst other common symptoms. I have also done the bi-carb soda test to check for low stomach acid, finding that I didn’t belch until 20 minutes after drinking the solution, indicating low acid levels. However, my blood tests come back normal for b12, Iron, and everything else really, despite having common symptoms of B12 and Iron deficiency? I don’t supplement either iron or b12, I take B12 through fortified foods and the only iron i get is through plant sources. Do you know whether blood tests are conclusive enough to identify certain deficiencies? Sorry for the long post, hope it isn’t too confusing!

Another thing you could do is try some digestive support to see if it helps. I wouldn’t use HCL without the supervision of a practitioner, but you can try bitters and a bit of ACV before meals to see if “boosting” the acidity of your stomach helps you digest your food better.

[…] fats, your gallbladder might need support. If you have trouble digesting meat, you might have too little stomach acid or a deficiency in digestive enzymes. If you have trouble digesting everything, you might have an […]

Hi Mickey! I am exploring whether there could be a connection to hair loss (eyelash and eyebrow) and low stomach acid. Like so many, I went to my family doctor with symptoms of indigestion and minor reflux. This was a few years ago. She prescribed Nexium and I was on it for a few years. It didn’t occur to me that low stomach acid was actually my problem, not excessive. I am menopausal and over the course of the past couple of years, I have experienced significant eyelash and brow thinning/loss. I have seen my doctor, dermatologist, Naturopath, eye specialists and nobody can determine why. I haven’t taken Nexium for a couple of years but wonder if the years I was on it prevented my body from absorbing essential nutrients and minerals, contributing to the hair loss. It is frustrating. I take vitamins and supplements and eat a healthy diet. I do experience digestive issues and constipation. I recently started taking Mastic Gum and DGL (Deglycyrrhizinated Licorce) which has helped. Any suggestions would be appreciated.

Hi Shawna! I think you are on the right track – our hair, skin, nails cannot form properly if we are not getting nutrients through the digestive process. Another thing to rule out would be hypothyroidism – thinning of the outer 1/3 of the eyebrows, especially can be related to that. Many folks with subclinical hypothyroidism see this symptom. Good luck!

[…] we have too much stomach acid. Actually, the opposite is true. Mickey from Autoimmune Wellness wrote a great article explaining how this works, but the quick summary is this: We need stomach acid to digest our food, […]

Hi Mickey! I want to come to the root cause of my Hashimotos and trying to get my thyroid numbers to where they have to be. For a couple of reasons I decided to do the home test for low stomach acid. I did the baking powder test 2 times and I didn’t belch at all. I will do the third test romorrow morning. I’ve been following AIP for the past 13 month, however, I was never on SAD and I also never had the need to eat acid reducers. I have successfully reintroduced a few things, such as walnuts and almonds, rice (only sticky so far). Any ideas, why I dod not belch? Thank you for your advice! The information on your site is invaluable! Vanja

Hi Vanja! I actually don’t do a baking powder test and can’t advise you on the results there – I would actually steer clear of any self tests and try and get evaluated by a practitioner if you think you may have an issue here. Another option would be gentle ways of supporting digestion to see if it gets you any mileage – things like herbal bitters, a bit of ACV before meals, etc. Good luck!

Hi, so glad to see this post….I was dx’d with Hashimoto’s in July 2016 having hashitoxicosis episode. Since then I have thyroid surges where I have lots of energy and then crash, have joint pain, extreme fatigue, etc. My question is I was just dx’d with low stomach acid and started on hcl with pepsin and also digestive enzymes. My stools are more normal so I’m excited about that. I’ve had stomach issues all my life and believe I’ve had malabsorption for several years, if this is a root cause of my hashimoto’s when could a person begin to see an improvement in symptoms? What liquid supplements would be good to try since I can’t break down pills as of yet?

Hey Jeannie! I’m not a medical practitioner, so just to be clear, this is a question best addressed by your functional doctor. I do think low HCL can be an underlying factor in nutrient deficiencies that certainly cause Hashimoto’s to flare, but I wouldn’t say resolving it is going to make your Hashimoto’s go away. It will certainly help you feel better though! If you are working with a doctor who is supervising your HCL use, I don’t see why that added acid won’t help you break down your supplements – unless they are recommending it specifically, I’m not sure you need to go the liquid route. Hope it helps!

I have chrons and I’m battling acid reflux right now. What things can I eat on AIP that aren’t going to agitate me? I ate some raw licorice, but I feel nauseous and the thought of eating vegetables, meat and or bone broth will agitate it more. Any advice would be greatly appreciated. Also, I think I have too much acid in my stomach right now.

Hey Glenda! I’m sorry but I can’t help troubleshoot medical issues. I would reach out to a practitioner to see if they can make some personalized recommendations for you – we have a listing over at aipcertified.com!

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